15-69793977-C-T

Variant names:

• chr15-69793977-C-T
• rs305039
• ENST00000647319.1:n.1229+817C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647319.1(DRAIC):​n.1229+817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 151,962 control chromosomes in the GnomAD database, including 43,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.75 (43820 hom., cov: 30)
• Consequence: DRAIC ENST00000647319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 3 publications found

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647319.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRAIC	ENST00000647319.1		n.1229+817C>T		intron	N/A
	DRAIC	ENST00000798860.1		n.127+37771C>T		intron	N/A
	DRAIC	ENST00000798861.1		n.106+37771C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114261 AN: 151844 Hom.: 43806 Cov.: 30

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.756

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.752 AC: 114311 AN: 151962 Hom.: 43820 Cov.: 30 AF XY: 0.746 AC XY: 55432 AN XY: 74274

African (AFR) AF: 0.687 AC: 28445 AN: 41392

American (AMR) AF: 0.688 AC: 10501 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2634 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2119 AN: 5148

South Asian (SAS) AF: 0.604 AC: 2897 AN: 4800

European-Finnish (FIN) AF: 0.823 AC: 8706 AN: 10576

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56346 AN: 67990

Other (OTH) AF: 0.749 AC: 1578 AN: 2106

Alfa AF: 0.791 Hom.: 76663

Bravo AF: 0.737

Asia WGS AF: 0.529 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.20
DANN	Benign	0.68
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs305039;

hg19: chr15-70086316;